Not sure what categories I am supposed to put credit card payments into.
For example right now I have 2 transactions pending approval. The -$12 coming from my checking account that was a credit card payment and the +$12 going to the credit card account. I'm not sure where these things should be categorized.
A $12 transfer from your on-budget chequing account to your on-budget credit card won't have a category.
Start in your chequing account register. In the Payee field, find your credit card account. When you select the account, YNAB will automatically populate the category with a "category not needed". Enter your outflow of $12. A corresponding inflow of $12 will automatically appear in your credit card register and the source will be your chequing account. YNAB has linked your cc payment utility to your cc account, so when you do this, the funds reserved for your payment will be reduced by the $12.